Transport of individual cells or chemical payloads on a subcellular scale is an enabling tool for the study of cellular communication, cell migration, and other localized phenomena. We present a magnetically actuated robotic system for the fully automated manipulation of cells and microbeads. Our strategy uses autofluorescent robotic transporters and fluorescently labeled microbeads to aid tracking and control in optically obstructed environments. We demonstrate automated delivery of microbeads infused with chemicals to specified positions on neurons.